Listening on http://127.0.0.1:32901 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user spfammatter Bfabric query: workflow containerid = 331 Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : query failed. Warning: Error in $: $ operator is invalid for atomic vectors 121: append 120: [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#125] 104: read_workflowid 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#135] 96: func 83: renderFunc 82: output$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 33197 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 4454 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4454 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 4454 Selected workflows ids: 4488 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4454 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4488 workflowtemplate step id 266 workflowtemplate step id 243 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 4454 Selected workflows ids: 4488 Selected workflows ids: 4508 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4454 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4488 workflowtemplate step id 266 workflowtemplate step id 243 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4508 workflowtemplate step id 254 workflowtemplate step id 254 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4454 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4488 workflowtemplate step id 266 workflowtemplate step id 243 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4508 workflowtemplate step id 254 workflowtemplate step id 254 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-33197.pdf bfabricUpload saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user cfortes Bfabric query: workflow containerid = 3322 Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : query failed. Warning: Error in $: $ operator is invalid for atomic vectors 121: append 120: [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#125] 104: read_workflowid 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#135] 96: func 83: renderFunc 82: output$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 33228 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 4484 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4484 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 4484 Selected workflows ids: 4515 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4484 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4515 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 4484 Selected workflows ids: 4515 Selected workflows ids: 4507 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4484 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4515 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4507 workflowtemplate step id 247 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 4484 Selected workflows ids: 4515 Selected workflows ids: 4507 Selected workflows ids: 4510 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4484 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4515 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4507 workflowtemplate step id 247 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = 4510 workflowtemplate step id 256 workflowtemplate step id 256 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4484 workflowtemplate step id 231 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4515 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4507 workflowtemplate step id 247 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4510 workflowtemplate step id 256 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-33228.pdf bfabricUpload generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4484 workflowtemplate step id 231 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4515 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4507 workflowtemplate step id 247 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4510 workflowtemplate step id 256 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-33228.pdf bfabricUpload saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user cfortes Bfabric query: workflow containerid = 33223 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 4478 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4478 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 4478 Selected workflows ids: 4479 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4478 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4479 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 4478 Selected workflows ids: 4479 Selected workflows ids: 4499 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4478 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4479 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4499 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 4478 Selected workflows ids: 4479 Selected workflows ids: 4499 Selected workflows ids: 4501 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4478 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4479 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4499 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = 4501 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4478 workflowtemplate step id 239 workflowtemplate step id 226 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4479 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4499 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4501 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-33223.pdf bfabricUpload generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4478 workflowtemplate step id 239 workflowtemplate step id 226 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4479 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4499 Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : query failed. Warning: Error in $: $ operator is invalid for atomic vectors 169: append 168: [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#189] 152: read_steptemplateid(input$workflowids[[x]]) 150: FUN [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#278] 149: lapply 148: eventReactiveValueFunc [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#278] 104: report 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#343] 96: func 83: renderFunc 82: output$downloadReportButton 1: runApp saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user cfortes Bfabric query: workflow containerid = 33223 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 4478 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4478 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 4478 Selected workflows ids: 4479 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4478 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4479 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 4478 Selected workflows ids: 4479 Selected workflows ids: 4516 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4478 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4479 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4516 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 4478 Selected workflows ids: 4479 Selected workflows ids: 4516 Selected workflows ids: 4517 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4478 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4479 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4516 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = 4517 workflowtemplate step id 256 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4478 workflowtemplate step id 239 workflowtemplate step id 226 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4479 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4516 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4517 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-33223.pdf bfabricUpload Execution halted